LAMMPS (27 Nov 2018)
  using 1 OpenMP thread(s) per MPI task
# 2d rounded polygon bodies

variable    r     index 4
variable    steps index 100000
variable    T     index 0.5
variable    P     index 0.1
variable    seed  index 980411

units       lj
dimension   2

atom_style  body rounded/polygon 1 6
atom_modify map array
read_data   data.squares
  orthogonal box = (0 0 -0.5) to (12 12 0.5)
  2 by 2 by 1 MPI processor grid
  reading atoms ...
  2 atoms
  2 bodies

replicate   $r $r 1
replicate   4 $r 1
replicate   4 4 1
  orthogonal box = (0 0 -0.5) to (48 48 0.5)
  2 by 2 by 1 MPI processor grid
  32 atoms
  Time spent = 0.000400782 secs

velocity    all create $T ${seed} dist gaussian mom yes rot yes
velocity    all create 0.5 ${seed} dist gaussian mom yes rot yes
velocity    all create 0.5 980411 dist gaussian mom yes rot yes

variable cut_inner  equal 0.5
variable k_n        equal 100
variable k_na       equal 2
variable c_n        equal 1
variable c_t        equal 1
variable mu         equal 0.1
variable delta_ua   equal 0.5

pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 1 1 ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 1 1 0.1 ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 1 1 0.1 0.5 ${cut_inner}
pair_style body/rounded/polygon 1 1 0.1 0.5 0.5
pair_coeff * * ${k_n} ${k_na}
pair_coeff * * 100 ${k_na}
pair_coeff * * 100 2

comm_modify vel yes

neighbor     0.5 bin
neigh_modify every 1 delay 0 check yes

timestep     0.001

#fix         1 all nve/body
#fix         1 all nvt/body temp $T $T 1.0
fix          1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0              y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
fix          1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0              y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0              y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0              y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0              y 0.001 0.1 1.0 couple xy fixedpoint 0 0 0

fix          2 all enforce2d

#compute      1 all body/local id 1 2 3
#dump         1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]

thermo_style custom step ke pe etotal press
thermo       1000

#dump	     2 all image 10000 image.*.jpg type type zoom 2.0 #             adiam 1.5 body type 0 0
#dump_modify  2 pad 6

run          ${steps}
run          100000
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 6.15685
  ghost atom cutoff = 6.15685
  binsize = 3.07843, bins = 16 16 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair body/rounded/polygon, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/2d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.774 | 4.774 | 4.774 Mbytes
Step KinEng PotEng TotEng Press 
       0     0.484375         0.25     0.734375 0.0067274306 
    1000   0.38428256 0.0014168922   0.38569945 0.0020468171 
    2000   0.41372193  0.015263236   0.42898517 0.0029343462 
    3000   0.54844547  0.014870378   0.56331585  0.001978353 
    4000   0.73816048  0.031668204   0.76982869 0.0025939718 
    5000   0.84536165  0.011504649    0.8568663 0.0037990517 
    6000   0.73776478   0.14445932    0.8822241 0.0086538113 
    7000   0.52022565  0.069507637   0.58973329 0.0072098694 
    8000   0.72653213   0.12783367   0.85436581  0.023907185 
    9000   0.87685728   0.12398193    1.0008392 0.0064591005 
   10000   0.72509641  0.097241969   0.82233837 0.0012418726 
   11000   0.62314955  0.056042914   0.67919247 0.0018880786 
   12000   0.57157436   0.18187429   0.75344865 0.0096135623 
   13000    0.7489742   0.08262775   0.83160195  0.009183917 
   14000   0.78835138   0.18761048   0.97596186  0.023684357 
   15000   0.40408761  0.079431327   0.48351893  0.025285348 
   16000    0.4071013   0.13207058   0.53917188   0.02015488 
   17000   0.48417067   0.16699781   0.65116848  0.059188189 
   18000   0.60038567   0.18317457   0.78356024 -0.046456387 
   19000   0.73796958  0.064271521    0.8022411  0.090257204 
   20000   0.62508659   0.14486336   0.76994994   0.04948543 
   21000    0.5596837   0.10018831   0.65987201  0.044961962 
   22000   0.30731517    0.1386103   0.44592547  0.015096596 
   23000   0.34371843    0.1486761   0.49239453  0.026100892 
   24000   0.33484204   0.25428479   0.58912683   0.01974393 
   25000   0.48714744   0.32743616    0.8145836  0.037925893 
   26000   0.33255994   0.29851422   0.63107417  0.049419529 
   27000   0.21735889   0.18816203   0.40552093  0.050622152 
   28000   0.31911317   0.12559898   0.44471215 -0.0036236361 
   29000   0.53280161  0.055185441   0.58798705  0.083856225 
   30000   0.52916941   0.28697284   0.81614225  0.055873213 
   31000   0.47861645   0.21932568   0.69794214   0.02762301 
   32000   0.46786314  0.041856438   0.50971958  0.029923804 
   33000   0.69944716  0.039356744    0.7388039  0.028174645 
   34000   0.39964317    0.1027175   0.50236068  0.039495865 
   35000   0.70199237   0.10421859   0.80621095  0.015943417 
   36000   0.45053533  0.078626602   0.52916193 0.0073950287 
   37000   0.41587918  0.056551665   0.47243084  0.034091318 
   38000   0.58663473  0.039228671    0.6258634  0.033093641 
   39000   0.72480658   0.14792564   0.87273222  0.030903741 
   40000   0.51163285   0.13445292   0.64608577  -0.03114559 
   41000   0.56273761   0.16720374   0.72994135  0.027968528 
   42000   0.61850184   0.10584389   0.72434573 -0.036301799 
   43000   0.60039772   0.11984289   0.72024062  0.080894236 
   44000   0.57499839  0.068211092   0.64320948  0.049726122 
   45000   0.69937239   0.16287141    0.8622438  0.044921114 
   46000   0.23303785    0.2391726   0.47221045  0.021668935 
   47000   0.27051781   0.10690378   0.37742159   0.11963476 
   48000     0.408895  0.079919688   0.48881469  0.087484004 
   49000   0.74363181  0.040819422   0.78445123  0.011937456 
   50000   0.84482316   0.10205256   0.94687572  0.064133262 
   51000   0.84923574  0.089882984   0.93911872  0.062696388 
   52000   0.66278324    0.0331554   0.69593864  0.035150337 
   53000   0.64737251  0.039608076   0.68698058  0.057687461 
   54000   0.68931435  0.042661403   0.73197576  0.069664795 
   55000   0.84523308   0.10293275   0.94816583  0.047343755 
   56000   0.80033937    0.1534797   0.95381907  0.070206074 
   57000    0.6214799    0.1174575    0.7389374  0.078530452 
   58000   0.64228495  0.088089896   0.73037485  0.060245994 
   59000   0.89376363  0.065171887   0.95893552  0.071658895 
   60000   0.90162992  0.016564761   0.91819468  0.089245946 
   61000   0.72439995 0.0076508835   0.73205083  0.031430213 
   62000   0.71590702 0.0046728326   0.72057986   0.10153514 
   63000   0.74491219 0.0046757926   0.74958798  0.077145851 
   64000   0.77173614  0.008265632   0.78000178 -0.049932265 
   65000   0.72789092 0.0053605745   0.73325149   0.27060389 
   66000   0.63001101  0.013871945   0.64388296  -0.17766692 
   67000   0.65887071 0.0069105692   0.66578128   0.31632918 
   68000   0.89042862 0.0026334652   0.89306209 -0.050495873 
   69000   0.83442374 0.0059232957   0.84034703  -0.21871692 
   70000   0.65149642  0.004885383   0.65638181   0.50428108 
   71000   0.66888808   0.01125057   0.68013865  -0.29575772 
   72000   0.74941609 0.0026616299   0.75207772   0.34800716 
   73000    0.7898844 0.0048982026    0.7947826 -0.096872644 
   74000   0.68823538 0.0021467794   0.69038216   0.12272852 
   75000    0.5238808 0.0046112795   0.52849208   0.25760316 
   76000   0.65512889  0.014567969   0.66969686  -0.24622674 
   77000   0.82292373 0.0092471048   0.83217083    0.4002304 
   78000   0.76305221   0.01101937   0.77407158  -0.10704945 
   79000   0.66279814 0.0090486405   0.67184678  0.037466134 
   80000   0.65808885  0.010000569   0.66808942   0.31742291 
   81000   0.91357798  0.046226814   0.95980479  -0.20945693 
   82000   0.87611859 -0.016794871   0.85932372   0.31759733 
   83000   0.66285455 -0.017921021   0.64493353   0.27065273 
   84000   0.67460715 -0.0076174891   0.66698966 -0.024772659 
   85000   0.77786135 0.0014316505     0.779293  -0.21635327 
   86000   0.83246393  0.087489797   0.91995372  -0.13431455 
   87000   0.62935573  0.045088823   0.67444455  0.037766395 
   88000   0.55264538 -0.024625272   0.52802011   0.18121213 
   89000   0.74171392 -0.012629926     0.729084  -0.27666424 
   90000   0.82542165  -0.02296567   0.80245598  -0.30497174 
   91000   0.72958657 -0.026275093   0.70331147  -0.27624518 
   92000    0.6319558  0.022568297   0.65452409  -0.33539318 
   93000   0.66685301  0.021889807   0.68874282  -0.39890762 
   94000   0.91243243 0.0078218509   0.92025428  -0.27213648 
   95000   0.81125179 -0.0096756295   0.80157616 -0.099802335 
   96000   0.63354907 -0.018329423   0.61521965   0.18199604 
   97000   0.66812347 -0.016650228   0.65147324   0.49878257 
   98000   0.81490013 -0.0049164866   0.80998365  -0.13473106 
   99000   0.82131147 0.0043198846   0.82563136   -0.3083957 
  100000   0.50880983 -0.010467027    0.4983428  0.060606332 
Loop time of 4.3169 on 4 procs for 100000 steps with 32 atoms

Performance: 2001435.573 tau/day, 23164.764 timesteps/s
95.1% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 1.2078     | 1.3972     | 1.6653     |  15.1 | 32.36
Neigh   | 0.0030954  | 0.003284   | 0.0034814  |   0.3 |  0.08
Comm    | 1.074      | 1.3595     | 1.6003     |  16.2 | 31.49
Output  | 0.001703   | 0.0030067  | 0.0068843  |   4.1 |  0.07
Modify  | 1.2071     | 1.2647     | 1.3062     |   3.6 | 29.30
Other   |            | 0.2893     |            |       |  6.70

Nlocal:    8 ave 9 max 6 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost:    17.75 ave 20 max 16 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Neighs:    14 ave 18 max 7 min
Histogram: 1 0 0 0 0 0 0 1 1 1

Total # of neighbors = 56
Ave neighs/atom = 1.75
Neighbor list builds = 1566
Dangerous builds = 0
Total wall time: 0:00:04
